抗冻蛋白冰水复合体系的分子动力学模拟
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摘要
抗冻蛋白是一种可以非依数性降低冰点,在低温环境中避免生物体冻伤产生的功能性蛋白.采用分子动力学模拟方法,通过计算体系总能量,从分子层面分析在冰水界面处吸附结合的云杉蚜虫抗冻蛋白、鳕鱼抗冻蛋白和非抗冻蛋白槲寄生毒蛋白对冰水界面的影响.研究结果表明,吸附在冰晶表面上的抗冻蛋白比非抗冻蛋白更容易使界面层体系中固相水分子转变为液相水分子.分析上述三种蛋白质氨基酸序列的亲疏水性特征,发现抗冻蛋白比非抗冻蛋白更容易使冰晶结合面形成类冰水层,诱导冰晶界面层的熔化.
Antifreeze proteins are functional proteins that can reduce the freezing point in nonequilibrium and avoid the freezing injury of organisms in low-temperature environment.The total energy of an ice-water interface system that with two kinds of antifreeze proteins and a kind of nonantifreeze protein(Choristoneura fumiferana(CfAFP),Zoarces americanus(ZaAFP)and non-antifreeze protein Viscum album)have been obtained respectively by using a molecular dynamics simulation method(MD).The effects of these proteins on the ice-water interface are analyzed.The results show that the antifreeze proteins adsorbed on the surface of ice crystals are much more likely to convert water molecules from solid phase into liquid phase water molecules in the interface layer system than non-antifreeze proteins.The hydrophilicity of the three kinds of protein sequences have been analyzed.It is found that antifreeze proteins can much more likely to form an ice-like layer on the ice-bound surface than non-antifreeze proteins,to induce the melting of the ice crystal interface layer.
Antifreeze proteins are functional proteins that can reduce the freezing point in nonequilibrium and avoid the freezing injury of organisms in low-temperature environment.The total energy of an ice-water interface system that with two kinds of antifreeze proteins and a kind of nonantifreeze protein(Choristoneura fumiferana(CfAFP),Zoarces americanus(ZaAFP)and non-antifreeze protein Viscum album)have been obtained respectively by using a molecular dynamics simulation method(MD).The effects of these proteins on the ice-water interface are analyzed.The results show that the antifreeze proteins adsorbed on the surface of ice crystals are much more likely to convert water molecules from solid phase into liquid phase water molecules in the interface layer system than non-antifreeze proteins.The hydrophilicity of the three kinds of protein sequences have been analyzed.It is found that antifreeze proteins can much more likely to form an ice-like layer on the ice-bound surface than non-antifreeze proteins,to induce the melting of the ice crystal interface layer.
引文
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[2]Li Q,Luo L.The kinetic theory of thermal hysteresis of a macromolecule solution[J].Chemical Physics Letters,1993,216(3/6):453-457.
[3]Li Q,Luo L.Further discussion on the thermal hysteresis of the ice growth inhibitor[J].Chemical Physics Letters,1994,223(3):181-184.
[4]Li Q,Luo L.Adsorption kinetics in the solution of a thermal hysteresis protein 1[J].Chemical Physics Letters,2000,320(3/4):335-338.
[5]Liu J,Li Q.A theoretical model on thermal hysteresis activity of the winter flounder protein‘HPLC-6’[J].Chemical Physics Letters,2003,378(3):238-243.
[6]Li Q Z,Yeh Y,Liu J J,et al.A two-dimensional adsorption kinetic model for thermal hysteresis activity in antifreeze proteins[J].Journal of Chemical Physics,2006,124(20):204702.
[7]Liu J,Li Q.Theoretical model of antifreeze protein-ice adsorption:Binding of large ligands to a two-dimensional homogeneous lattice[J].Chemical Physics Letters,2006,422(1):67-71.
[8]Li L F,Liang X X,Li Q Z.The thermal hysteresis activity of the type I antifreeze protein:A statistical mechanics model[J].Chemical Physics Letters,2009,472(1/3):124-127.
[9]Griffith M,Ewart K V.Antifreeze proteins and their potential use in frozen foods[J].Biotechnology Advances,1995,13(3):375-402.
[10]文玉华,朱如曾,周富信,等.分子动力学模拟的主要技术[J].力学进展,2003,33(1):65-73.
[11]Haymet A,Ward L,Harding M,et al.Valine substituted winter flounder'antifreeze':Preservation of ice growth hysteresis[J].Febs Letters,1998,430(3):301-6.
[12]Nada H,Furukawa Y.Antifreeze proteins:computer simulation studies on the mechanism of ice growth inhibition[J].Polymer Journal,2012,44(7):690-698.
[13]Todde G,Whitman C,Hovm?ller S,et al.Induced ice melting by the snow flea antifreeze protein from molecular dynamics simulations.[J].Journal of Physical Chemistry B,2014,118(47):13527.
[14]Liu K,Wang C,Ma J,et al.Janus effect of antifreeze proteins on ice nucleation[J].Proc Natl Acad Sci U S A,2016,113(51):14739-14744.
[15]Berendsen H J C,Spoel D V D,Drunen R V.GROMACS:A message-passing parallel molecular dynamics implementation[J].Computer Physics Communications,1995,91(1/3):43-56.
[16]Jorgensen W L,Chandrasekhar J,Madura J D,et al.Comparison of simple potential functions for simulating liquidwater[J].Journal of Chemical Physics,1983,79(2):926-935.
[17]Jorgensen W L,And D S M,Tiradorives J.Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids[J].J am chem soc,1996,118(45):11225-11236.
[18]Darden T,York D,Pedersen L.Particle mesh Ewald:An N·log(N)method for Ewald sums in large systems[J].Journal of Chemical Physics,1993,98(12):10089-10092.
[19]Hess B,Bekker H,Berendsen H J C,et al.LINCS:A linear constraint solver for molecular simulations-Hess-1998-Journal of Computational Chemistry-Wiley Online Library[J].Journal of Chemical Theory&Computation,2008,4(1):1463-1472.
[20]Parrinello M,Rahman A.Polymorphic transitions in single crystals:A new molecular dynamics method[J].Journal of Applied Physics,1981,52(12):7182-7190.
[21]Shūichi Nosé.A molecular dynamics method for simulations in the canonical ensemble[J].Molecular Physics,2002,52(2):255-268.
[22]Todde G,Hovm?ller S,Laaksonen A.Influence of antifreeze proteins on the ice/water interface[J].Journal of Physical Chemistry B,2015,119(8):3407-13.
[23]Hayward J A,Haymet A D J.The ice/water interface:orientational order parameters for the basal,prism,{20&unknown;21,and{2&unknown;1&unknown;10interfaces of ice Ih[J].Physical Chemistry Chemical Physics,2002,4(15):3712-3719.
[24]Leinala E K,Davies P L,Doucet D,et al.Aβ-Helical Antifreeze Protein Isoform with Increased Activity[J].Journal of Biological Chemistry,2002,277(36):33349-33352.
[25]Jia Z,Deluca C I,Chao H,et al.Structural basis for the binding of a globular antifreeze protein to ice[J].Nature,1996,384(6606):285-8.
[26]Wagner H,Jordan E.An immunologically active arabinogalactan from Viscum album,‘berries’[J].Phytochemistry,1988,27(8):2511-2517.
[27]Berman H M,Westbrook J,Feng Z,et al.The Protein Data Bank[J].Genetica,2000,106(1/2):149-158.
[28]Fernández R G,Abascal J L F,Vega C.The melting point of ice Ih for common water models calculated from direct coexistence of the solid-liquid interface[J].Journal of Chemical Physics,2006,124(14):144-342.